


Agents of SHIELD- A New World: The First Day

by kamenrangerxvi01



Series: Earth-199999-Alpha Omnibus [20]
Category: Agents of S.H.I.E.L.D. (TV), Marvel Cinematic Universe
Genre: Alternate History, Divergent Timelines, F/F, SHIELD
Language: English
Status: Completed
Published: 2019-12-10
Updated: 2019-12-10
Packaged: 2021-02-25 22:06:53
Rating: Not Rated
Warnings: No Archive Warnings Apply
Chapters: 3
Words: 2,799
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/21742678
Author URL: https://archiveofourown.org/users/kamenrangerxvi01/pseuds/kamenrangerxvi01
Summary: It's Skye Simmons-Johnson's first day as a probationary SHIELD Agent.She's been assigned to the MUSEUM facility to help Agent Scott Riley deal with the place, as he teachers her about life in SHIELD and on the new Earth she's chosen to call home.(Setting: Late August 2018, within a few days after the ending of the main story of "Operation Exiles"; leads into another story.)
Relationships: Jemma Simmons/Skye | Daisy Johnson
Series: Earth-199999-Alpha Omnibus [20]
Series URL: https://archiveofourown.org/series/1191670
Kudos: 2





	1. Chapter 1

“This is a big responsibility.” Fury said.

“I know, Uncle Nick.” Scott said “I promise to feed her and walk her every day.”

“That is so not funny” Skye said, standing off the side.

“Being an S.O. isn’t a joke Scott.” Fury continued.

“Sorry, sir”

The older man turned to Skye and handed her a small box, which she opened to find her own badge.

“Welcome to S.H.I.E.L.D., Probationary Agent Johnson.”

“Thank you, sir!” The girl snapped to attention and saluted.

She stood there for a moment as Scott and Fury just looked at her.

“I don’t need to do all this, do I?” She asked.

The two men shook their heads. “the ‘Sir.’ Yes. The rest, no” Scott said, before pointing at Fury. “And for the record, only to him.”

“This is going to take some getting used to.” She said “And, um, sir, my wife and I decided on ‘Simmons-Johnson’ as our last name.”

“Ok, I’ll make a note of that.” Fury said, turning to Scott. “I need to head out. Meetings to have, people to see. She’s all yours Scott.”

“Ok…” Scott said, rubbing his hands together as his godfather left his office and headed out to the street.

“You have no idea what you’re doing, do you?” Skye asked.

“Not a clue.” He admitted “I’ve never been anyone’s supervising anything before. They wouldn’t let me even watch the class gerbil for five minutes…”

“So is there like a handbook or something?”

“Probably one down in the library.” He said “Probibly years out of date, but it would be a start.”

“You have a library?”

“Oh… right…” Scott said, “you’ve not actually been downstairs yet.”

“Yeah I was, that’s where you found me. Remember?”

“No, I mean DOWNSTAIRS downstairs…Come on.”

He led Skye out of the office and down the hall to an old looking elevator, complete with gate and manual control handle.

He locked the gate and turned the controls on, causing the car to bounce slightly.

“Ok, that’s not supposed to happen.” He said as he tried again, only for it to continue bouncing.

“Great first day…” Skye said.

“Oh… wait. I got it. it set to up. We’re at the top of the shaft, no place to go.” He reset the controls. “Here we go. Going down.”

“So from the street, you have to go to the roof, and come back down again?”

“You should have seen the Fridge…” he said as they got underway “The other elevator, the larger one we use to go in and out, that one is supposed to go downstairs as well, I just haven’t cut open the shaft yet at the bottom.”

The elevator passed the other floors and the basements of the building before the shaft opened up to a wide, deep, open space.

Scott stopped at the first floor.

“Sub level 1, housewares, ladies’ lingerie and open jaws wide enough to catch flies…”

Skye stepped out into the catwalk before her. They were at the top of a deep, deep pit, with a ring shaped catwalk built on steel work in the center. On the side of the ring where the elevator stopped, the wall was solid, but at the other three points to the left, right, and far side, were opening cut into the rocks. Every level seemed to be like this.

“How deep is this place?” She asked, looking over the edge.

“It’s basically an upside-down skyscraper. Fifty sub-levels, though not all of them are used. Some aren’t even finished as best as I can tell. This was one of the first dedicated facilities constructed by SHIELD after it was converted from the SSR. They dug down into bed rock and blasted out this hole.”

“Seems like a lot for a storage facility that early.”

“From what little documentation I’ve found, it was meant to be used as a main operations base, close to the UN but not too close. Since it’s on what was then pre-existing government property, Navy didn’t sell the yard to the city till 1970, nobody noticed or cared. I think the plan was to leave the Camp Lehigh base and move here, but that fell apart.”

“Best you can tell? I though you knew everything.” She said, teasing him.

“I might be an amateur agency historian, but there are things well and truly outside my prevue. Even Zeros don’t know everything. The Lighthouse was completely off the books. Otherwise I would have hidden there the moment the shit hit the fan.”

“So this place was off the records?”

“No. At least it wasn’t supposed to be. There was a fire here, while it was abandoned, wiped out a lot of old files. Areas seem to have gotten converted into storage not long after construction commenced, I think there was some budgetary issues or something, and it was abandoned completely when plans for the Triskelion were first put forward. They capped the elevator shafts and left this place as and unintentional time capsule.

“This entire framework we’re standing on was meant to be the backbone of a larger building, a lot like the Lighthouse.”

“How’d you find it?”

“I should really introduce you to the Koenig’s one day…” He said “They found a few documents referencing the place a few months ago in another one of their storage facilities. Follow me.”


	2. Chapter 2

He led her around to the first bridge into the wall to their right.

“First stop, the motor pool, or, as I like to call it, the garage Jay Leno _wishes_ he had…”

“Who?”

“Sorry…Never mind… I’ll explain later.”

The room’s floor was cut away, showing it actually went down four floors, with ramps dug into the walls connecting each level, and a large elevator door on the far side, the one Scott had mentioned before, still plugged with reinforced concrete. Each level had two decks, with cars on the lower level needing to be moved out of the way to lower the top deck. All in all, Scott’s count left them with over 500 vehicles of various sizes, makes and models, ranging from pre-war all the way to the base’s complete abandonment in the late 1970s/early 1980s.

“Best I can figure, this was supposed to be employee parking had the original concept for this as an actual base been realized.”

Skye wandered into the large room and noticed a specific car.

“A Packard Super Eight…” She said, whipping the dust from the windshield. “My dad had one of these. I asked Jas to marry me the first time in the back seat.”

“It’s yours if you want it.” Scott said

“Seriously?” She asked “Didn’t know an SO could do that…”

“Half the reason I’m here is to tally what’s in storage here. If I don’t count it, it doesn’t exist, now, does it? Just be careful, replacement parts for this are going to be hard to come by. We might actually have to make some of them.”

“I could just go to a dealer…”

“Packard hasn’t made cars in decades.”

“Shit… Ok, that is going to make this hard…”

“Tell you what. Why don’t you just think about it. I’ll leave it for you. You could fix it in your spare time.”

“I don’t think I’m going to be having much of that…” She said, thinking about her newborn twins upstairs with Jas.

“Well…” Scott said, not knowing what else to say, “Let’s keep going.”

He led her around to one of the other openings and took a flashlight off his belt.

“This seems to have been intended as the main elevator bank.”

“How can you tell?”

“The holes in the floor…” he said, shining the light around, pointing at the gaps he’s taped off with caution tape and blocked with loose wood.

“This was probably going to be a big place…”

“Well, like I said, UN is nearby. SHIELD used to reach far and wide.”

“How important is it that we’re near the UN? Rogers just used it as a way to enforce his will on other countries.”

“What did I tell you?”

“I didn’t realize ‘Different lives, different paths applied to something that big.”

Scott just shone his light in her face

“Have you been even remotely paying attention?” He asked “The UN’s place in the world… it’s sorta… it’s… I’m just going to say it’s complicated for now and I’ll leave it at that because this supposed to a job orientation, not a world history lesson.”

He led her back to the working elevator, past the last bay full of old furniture and took her down a few levels.

“the other bays on sublevels 2 and 3 I’ve set aside for weapons storage, 4 was empty, so I moved all the loose construction equipment I’ve found there.” He said as they passed those floors before stopping again.

“Sublevel 5. Document storage A…” He said, pointing with the flashlight. “that’s where the fire was.”

“How did it start?” She asked as they walked towards it “I thought you said the place was sealed?”

“I’m not a forensic fire investigator, but best our guys were able to tell from the scans I took, a colony of rats got in, took up residence down here sometime in the mid 90s. One chewed through a live cable and got zapped, the spark caught some paper they’d used as nesting material, caused the entire room to go up in flames.”

Skye looked into the room. “Still smells in here.” She noted.

The two returned to the elevator and went down another level.

“Now, from here on down, is where stuff gets interesting.” He said “Instead of simple holes in the walls into bays, we get actuall tunnels branching off. We’re deep enough to avoid disturbing anything.”

They stepped off and Scott led her down one of the tunnels. Both sides of the passage were lined with boxes of various sizes and shapes.

“So, you’ve spent the past few months just going through all these?”

“In short, yes.” He said. He pulled the top of one box off and pulled out one of the items inside “Want a three-ring binder? I’ve got over four hundred.”

“Jesus…”

“Would you like to see my 1500 cases of loose-leaf paper?”

“I though you said this was an archive of your old stuff. Not office supply land.”

“This is just one part of the wonderful world I’m in charge of. They stored every and anything they didn’t need down here. I’ve got about two million useless ballpoint pens.” He said, before leading her back to the elevator.

“Tell you what… You want secrets and mysteries… Follow me.”

Scott brought them down to sublevel 27. He quietly walked down a dark, dank passageway. They eventually ended up a large, heavy looking door.

“What’s in there?” Skye asked.

Scott looked back at her. “I have no idea at all.” He said with a smile.

“You can’t get it open?”

“I haven’t really tried… Want to give it a spin?”

He touched her hand to duplicate her powers, and the two set to work vibrating the big, steel door.”

“It’s working!” Scott yelled.

The heavy door came loose and fell forward at the pair’s feet…

Followed by a massive torrent of water.


	3. Chapter 3

The rush of water struck the two and carried them back down the passage. They narrowly avoided certain doom by grabbing onto the railings of the central shaft and pulling themselves clear.

“OK… I think class dismissed for now…” Scott said.

Scott quickly went up a to one of the storage bays and returned with a large gun like device.

“Help me hold this steady” he said, resting it on the railing.

The two held on as Scott pulled the trigger. A large blob was launched across the room, sticking to the wall and expanding into a seal, holding the water back.

“Well… Exciting first day…” Skye said as the two dumped the sealing gun on the walkway and caught their breaths.

“And… take a guess what’s the one thing I’ve yet to find down here…”

Skye thought for a second.

“A pump.” He said. “We need to seal the leak and then pump out all the water. But, first things’s first, we get out of these wet clothes.”

“What in God’s name happened to the two of you?” Jas asked as the pair climbed back into Zephyr Zero, both still sopping wet. “You smell like something died.”

“We went for an unplanned swim.” Scott said as he headed into his bunk to change.

“So, anything interesting down there not currently soaking in toxic sludge?” Jas asked reacting as Skye came closer, “You two are really going to need a shower.”

“Well… I guess it can be a surprise.” Skye said.

“Great.” Jas said “Shower. Now.”

“Yes dear…” Skye said before marching back into the bathroom.

“This doesn’t look or smell anything like what my mom used to make.” Skye said as she looked at the food on her plate.

“I’m guess you guys didn’t eat out much?” Scott said between bites of his General Tso’s chicken. She shook her head.

“I spoke to Mack” He continued “They’re bringing me a pump tomorrow and then taking you back up to the Lighthouse for some onboarding program.”

“I thought that was your job?” Skye asked “Besides, I can’t leave Jas and the kids. I thought you said they had parental leave on this Earth?”

“Yeah,” Jas chimed in, “how are we supposed to bond with our children if she’s hopping around all the time?”

At that point, little Daisy began to fuss.

“I can’t just leave her like this.”

“I can call my mom?” Scott offered. “Look, I’m sorry, this is what Fury, Mack and May decided. Truth be told, I think Fury needs me to take care of something tomorrow for him, so it’s probably going to be for the best. They want you up there tomorrow. It’s only going to be overnight. Maybe you could go all go. I don’t know. We’re going to have to figure that out.”

The next day, after much discussion, Jas figured she could make the overnight alone with the twins and Skye left when the quinjet carrying the heavy-duty pump returned to base.

She spent the flight going over the recommended reading Scott had given her. The text of the Sokovia Accords.

“Hey sis!” Daisy said, giving her twin a hug as she came down the ramp.

“I wonder if I’ll ever get used to this.” Skye said, looking her living mirror image.

“Welcome back, Agent.” May said with a nod.

“Do I have to call you ma’am?” Skye asked.

“I don’t know, do you like having have two working legs?” May said deadpan

Skye tensed up, like she was in trouble.

“Relax, Skye, I was kidding. No, you don’t have to call me that.”

Daisy brought Skye downstairs and sat her down to eat.

“So, how’s things?” Daisy asked. She could see the bags under her sister’s eyes, she wasn’t sleeping much.

“They seem to be organized. They’re taking turns waking up just as we’re falling back to sleep.” Skye said “They’ve already mastered the art of psychological warfare... But I wouldn’t trade being a mom for anything.”

“Dad, here, owned a building in Milwaukee. I’ve put it up for sale. Got some offers. I want to use the money to buy you two a place to live. I also want to put some of the money in a trust fund, so you’d never have to worry about property taxes.”

“Wow… how much are we talking?”

“Several million.”

“wow…” Skye said, impressed.

“Don’t go thinking I could get you a place on Park Avenue. I want to save some of this. For, you know… If Scott and I… if things work out.”

After eating, the two sat and talked for quite some time before May came and took her downstairs.

“So, is there a reason you called me back here other than to visit with Daisy?” Skye asked as May led her down the corridor.

“Since you’re an ‘agent with powers’, we’re required under the Sokovia accords to give you training in your powers. It’s an official audit thing, something Scott couldn’t do on his own. It’s just a formality.” She led Skye into a room set up with desks.

Skye sat down and waited, going back to the book Scott had given her.

Eventually, she heard Fury coming down the corridor.

“Meet your classmate…” Fury said as the door opened.

She got up and walked toward the door. Fury was leading a young man inside.

“Hi, I’m Skye.” She said, offering to shake hands.

“I’m Peter.” He said.

“Peter Parker.”

To Be continued in

"Spider-Man: Divided Loyalties"


End file.
